Our robot and controller are randomly disconnecting from VEXnet for around 3-5 seconds at a time, it'll be running fine up until then and then just drop connection, our controller batteries are at yellow and will be charged in the morning, is that the problem or is there a bigger problem? also I just paired the robot and controller together today could that be what's causing this also?

I would definitely check the batteries first and foremost, as low batteries in any robotics system can cause a slew of problems. Next, I would suggest swapping out the VEXNet keys, if possible, to help determine if they could possibly be the source of the problem.

Finally, try pairing the Cortex and VEXNet controller again to see if the pairing could be the problem (it is unlikely that this is the issue, though, if the Cortex and Joystick Controller are communicating with one another).